Mercurial > repos > devteam > tabular_to_fastq

diff tabular_to_fastq.py @ 4:2dcfbbf9071a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
author iuc
date Wed, 19 Feb 2020 12:59:28 -0500
parents b8cdc0507586
children
line wrap: on
line diff
--- a/tabular_to_fastq.py	Fri Nov 01 13:27:30 2019 -0400
+++ b/tabular_to_fastq.py	Wed Feb 19 12:59:28 2020 -0500
@@ -14,15 +14,14 @@
     max_col = max(identifier_col, sequence_col, quality_col)
     num_reads = None
     skipped_lines = 0
-    out = open(output_filename, 'w')
-    for num_reads, line in enumerate(open(input_filename)):
-        fields = line.rstrip('\n\r').split('\t')
-        if len(fields) > max_col:
-            out.write("@%s\n%s\n+\n%s\n" % (fields[identifier_col], fields[sequence_col], fields[quality_col]))
-        else:
-            skipped_lines += 1
+    with open(output_filename, 'w') as out:
+        for num_reads, line in enumerate(open(input_filename)):
+            fields = line.rstrip('\n\r').split('\t')
+            if len(fields) > max_col:
+                out.write("@%s\n%s\n+\n%s\n" % (fields[identifier_col], fields[sequence_col], fields[quality_col]))
+            else:
+                skipped_lines += 1
 
-    out.close()
     if num_reads is None:
         print("Input was empty.")
     else: